Functional genomics of membrane transporters in human populations

Genome Research

Volumn 16, Issue 2, 2006, Pages 223-230

  Urban, Thomas J ^a   Sebro, Ronnie ^a   Hurowitz, Evan H ^a   Leabman, Maya K ^a   Badagnani, Ilaria ^a   Lagpacan, Leah L ^a   Risch, Neil ^a   Giacomini, Kathleen M ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; CARRIER PROTEIN; MEMBRANE PROTEIN;

ARTICLE; CELL ASSAY; CHEMICAL ANALYSIS; CONTROLLED STUDY; DNA DETERMINATION; DNA SCREENING; ETHNIC DIFFERENCE; ETHNIC GROUP; FUNCTIONAL GENOMICS; GENE EXPRESSION SYSTEM; GENE FREQUENCY; GENETIC CONSERVATION; GENETIC POLYMORPHISM; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; HETEROLOGOUS EXPRESSION; HUMAN; HUMAN CELL; MEMBRANE TRANSPORT; MOLECULAR EVOLUTION; PHENOTYPIC VARIATION; POPULATION GENETICS; PRIORITY JOURNAL; PROTEIN DEFECT; PROTEIN FUNCTION; PROTEIN VARIANT; QUANTITATIVE ANALYSIS; QUANTITATIVE GENETICS; SAMPLE; TRANSPORT KINETICS;

BIOLOGICAL TRANSPORT; ETHNIC GROUPS; GENE EXPRESSION; GENE FREQUENCY; GENOMICS; HUMANS; MEMBRANE TRANSPORT PROTEINS; POLYMORPHISM, GENETIC;

EID: 32044435382     PISSN: 10889051     EISSN: 15495469     Source Type: Journal    
DOI: 10.1101/gr.4356206     Document Type: Article

References (41)

1. Badagnani, I., Chan, W., Castro, R.A., Brett, C.M., Huang, C.C., Stryke, D., Kawamoto, M., Johns, S.J., Ferrin, T.E., Carlson, E.J., et al. 2005. Functional analysis of genetic variants in the human concentrative nucleoside transporter 3 (CNT3; SLC28A3). Pharmacogenomics J. 5: 157-165.
2. Botstein, D. and Risch, N. 2003. Discovering genotypes underlying human phenotypes: Past successes for mendelian disease, future approaches for complex disease. Nat. Genet. 33: 228-237.
3. Cargill, M., Altshuler, D., Ireland, J., Sklar, P., Ardlie, K., Patil, N., Lane, C.R., Lim, E.P., Kalayanaraman, N., Nemesh, J., et al. 1999. Characterization of single-nucleotide polymorphisms in coding regions of human genes. Nat. Genet. 22: 231-238.
4. Chasman, D. and Adams, R.M. 2001. Predicting the functional consequences of non-synonymous single nucleotide polymorphisms: Structure-based assessment of amino acid variation. J. Mol. Biol. 307: 683-706.
5. Cohen, J.C., Kiss, R.S., Pertsemlidis, A., Marcel, Y.L., McPherson, R., and Hobbs, H.H. 2004. Multiple rare alleles contribute to low plasma levels of HDL cholesterol. Science 305: 869-872.
6. Cooper, G.M., Brudno, M., Green, E.D., Batzoglou, S., and Sidow, A. 2003. Quantitative estimates of sequence divergence for comparative analyses of mammalian genomes. Genome Res. 13: 813-820.
7. Fay, J.C., Wyckoff, G.J., and Wu, C.I. 2001. Positive and negative selection on the human genome. Genetics 158: 1227-1234.
8. Fujita, T., Brown, C., Carlson, E.J., Taylor, T., de la Cruz, M., Johns, S.J., Stryke, D., Kawamoto, M., Fujita, K., Castro, R., et al. 2005. Functional analysis of polymorphisms in the organic anion transporter, SLC22A6 (OAT1). Pharmacogenet. Genomics 15: 201-209.
9. Gonzalez, F.J., Skoda, R.C., Kimura, S., Umeno, M., Zanger, U.M., Nebert, D.W., Gelboin, H.V., Hardwick, J.P., and Meyer, U.A. 1988. Characterization of the common genetic defect in humans deficient in debrisoquine metabolism. Nature 331: 442-446.
10. Grantham, R. 1974. Amino acid difference formula to help explain protein evolution. Science 185: 862-864.
11. Gray, J.H., Mangravite, L.M., Owen, R.P., Urban, T.J., Chan, W., Carlson, E.J., Huang, C.C., Kawamoto, M., Johns, S.J., Stryke, D., et al. 2004. Functional and genetic diversity in the concentrative nucleoside transporter, CNT1, in human populations. Mol. Pharmacol. 65: 512-519.
12. Halushka, M.K., Fan, J.B., Bentley, K., Hsie, L., Shen, N., Weder, A., Cooper, R., Lipshutz, R., and Chakravarti, A. 1999. Patterns of single-nucleotide polymorphisms in candidate genes for blood-pressure homeostasis. Nat. Genet. 22: 239-247.
13. Hartl, D.L. and Clark, A.G. 1997. Principles of population genetics. Sinauer Associates, Sunderland, MA.
14. Hirschhorn, J.N. and Altshuler, D. 2002. Once and again-issues surrounding replication in genetic association studies. J. Clin. Endocrinol. Metab. 87: 4438-4441.
15. Hirschhorn, J.N., Lohmueller, K., Byrne, E., and Hirschhorn, K. 2002. A comprehensive review of genetic association studies. Genet. Med. 4: 45-61.
16. Howard, H.C., Mount, D.B., Rochefort, D., Byun, N., Dupre, N., Lu, J., Fan, X., Song, L., Riviere, J.B., Prevost, C., et al. 2002. The K-Cl cotransporter KCC3 is mutant in a severe peripheral neuropathy associated with agenesis of the corpus callosum. Nat. Genet. 32: 384-392.
17. Leabman, M.K., Huang, C.C., Kawamoto, M., Johns, S.J., Stryke, D., Ferrin, T.E., DeYoung, J., Taylor, T., Clark, A.G., Herskowitz, I., et al. 2002. Polymorphisms in a human kidney xenobiotic transporter, OCT2, exhibit altered function. Pharmacogenetics 12: 395-405.
18. Leabman, M.K., Huang, C.C., DeYoung, J., Carlson, E.J., Taylor, T.R., de la Cruz, M., Johns, S.J., Stryke, D., Kawamoto, M., Urban, T.J., et al. 2003. Natural variation in human membrane transporter genes reveals evolutionary and functional constraints. Proc. Natl. Acad. Sci. 100: 5896-5901.
19. Lockridge, O. 1990. Genetic variants of human serum cholinesterase influence metabolism of the muscle relaxant succinylcholine. Pharmacol. Ther. 47: 35-60.
20. Miller, M.P. and Kumar, S. 2001. Understanding human disease mutations through the use of interspecific genetic variation. Hum. Mol. Genet. 10: 2319-2328.
21. Muller, T., Rahmann, S., and Rehmsmeier, M. 2001. Non-symmetric score matrices and the detection of homologous transmembrane proteins. Bioinformatics 17: S182-S189.
22. Ng, P.C. and Henikoff, S. 2001. Predicting deleterious amino acid substitutions. Genome Res. 11: 863-874.
23. _. 2002. Accounting for human polymorphisms predicted to affect protein function. Genome Res. 12: 436-446.
24. _. 2003. SIFT: Predicting amino acid changes that affect protein function. Nucleic Acids Res. 31: 3812-3814.
25. Ng, P.C., Henikoff, J.G., and Henikoff, S. 2000. PHAT: A transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics 16: 760-766.
26. Osato, D.H., Huang, C.C., Kawamoto, M., Johns, S.J., Stryke, D., Wang, J., Ferrin, T.E., Herskowitz, I., and Giacomini, K.M. 2003. Functional characterization in yeast of genetic variants in the human equilibrative nucleoside transporter, ENT1. Pharmacogenetics 13: 297-301.
27. Owen, R.P., Gray, J.H., Taylor, T.R., Carlson, E.J., Huang, C.C., Kawamoto, M., Johns, S.J., Stryke, D., Ferrin, T.E., and Giacomini, K.M. 2005. Genetic analysis and functional characterization of polymorphisms in the human concentrative nucleoside transporter, CNT2. Pharmacogenet. Genomics 15: 83-90.
28. Pascual, J.M., Wang, D., Lecumberri, B., Yang, H., Mao, X., Yang, R., and De Vivo, D.C. 2004. GLUT1 deficiency and other glucose transporter diseases. Eur. J. Endocrinol. 150: 627-633.
29. Patil, N., Berno, A.J., Hinds, D.A., Barrett, W.A., Doshi, J.M., Hacker, C.R., Kautzer, C.R., Lee, D.H., Marjoribanks, C., McDonough, D.P., et al. 2001. Blocks of limited haplotype diversity revealed by high-resolution scanning of human chromosome 21. Science 294: 1719-1723.
30. Ramensky, V., Bork, P., and Sunyaev, S. 2002. Human non-synonymous SNPs: Server and survey. Nucleic Acids Res. 30: 3894-3900.
31. Risch, N.J. 2000. Searching for genetic determinants in the new millennium. Nature 405: 847-856.
32. Risch, N., Burchard, E., Ziv, E., and Tang, H. 2002. Categorization of humans in biomedical research: Genes, race and disease. Genome Biol. 3: comment2007.
33. Shu, Y., Leabman, M.K., Feng, B., Mangravite, L.M., Huang, C.C., Stryke, D., Kawamoto, M., Johns, S.J., DeYoung, J., Carlson, E., et al. 2003. Evolutionary conservation predicts function of variants in the human organic cation transporter, OCT1. Proc. Natl. Acad. Sci. 100: 5902-5907.
34. Stephens, J.C., Schneider, J.A., Tanguay, D.A., Choi, J., Acharya, T., Stanley, S.E., Jiang, R., Messer, C.J., Chew, A., Han, J.H., et al. 2001. Haplotype variation and linkage disequilibrium in 313 human genes. Science 293: 489-493.
35. Sunyaev, S., Ramensky, V., and Bork, P. 2000. Towards a structural basis of human non-synonymous single nucleotide polymorphisms. Trends Genet. 16: 198-200.
36. Sunyaev, S., Ramensky, V., Koch, I., Lathe III, W., Kondrashov, A.S., and Bork, P. 2001. Prediction of deleterious human alleles. Hum. Mol. Genet. 10: 591-597.
37. Sunyaev, S., Kondrashov, F.A., Bork, P., and Ramensky, V. 2003. Impact of selection, mutation rate and genetic drift on human genetic variation. Hum. Mol. Genet. 12: 3325-3330.
38. Tajima, F. 1989. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
39. Vaisse, C., Clement, K., Guy-Grand, B., and Froguel, P. 1998. A frameshift mutation in human MC4R is associated with a dominant form of obesity. Nat. Genet. 20: 113-114.
40. Wang, Z. and Moult, J. 2001. SNPs, protein structure, and disease. Hum. Mutat. 17: 263-270.
41. Yeo, G.S., Farooqi, I.S., Aminian, S., Halsall, D.J., Stanhope, R.G., and O'Rahilly, S. 1998. A frameshift mutation in MC4R associated with dominantly inherited human obesity. Nat. Genet. 20: 111-112.